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1. The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula

   https://doi.org/10.1111/tpj.16626  

   Roy, Sonali; Torres‐Jerez, Ivone; Zhang, Shulan; Liu, Wei; Schiessl, Katharina; Jain, Divya; Boschiero, Clarissa; Lee, Hee‐Kyung; Krom, Nicholas; Zhao, Patrick X; et al (May 2024, The Plant Journal)

   SUMMARY The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root‐like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide‐coding genes inMedicago truncatula. Five out of fifteen GLV/RGF genes were notably upregulated during nodule organogenesis and were differentially responsive to nitrogen deficiency and auxin treatment. Specifically, the expression ofMtGLV9andMtGLV10at nodule initiation sites was contingent upon the NODULE INCEPTION transcription factor. Overexpression of these five nodule‐induced GLV genes in hairy roots ofM. truncatulaand application of their synthetic peptide analogues led to a decrease in nodule count by 25–50%. Uniquely, the GOLVEN10 peptide altered the positioning of the first formed lateral root and nodule on the primary root axis, an observation we term ‘noduletaxis’; this decreased the length of the lateral organ formation zone on roots. Histological section of roots treated with synthetic GOLVEN10 peptide revealed an increased cell number within the root cortical cell layers without a corresponding increase in cell length, leading to an elongation of the root likely introducing a spatiotemporal delay in organ formation. At the transcription level, the GOLVEN10 peptide suppressed expression of microtubule‐related genes and exerted its effects by changing expression of a large subset of Auxin responsive genes. These findings advance our understanding of the molecular mechanisms by which GOLVEN peptides modulate root morphology, nodule ontogeny, and interactions with key transcriptional pathways. 

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2. p ‐Chloropropynyl Phenylalanine, a Versatile Non‐Canonical Amino Acid for Co‐Translational Peptide Macrocyclization and Side Chain Diversification

   https://doi.org/10.1002/cbic.202300020  

   Osorio Franco, H. Estheban; Le, Anthony V.; Chang, Nathan Y.; Hartman, Matthew C. (June 2023, ChemBioChem)

   Abstract Macrocyclization has proven to be a beneficial strategy to improve upon some of the disadvantages of peptides as therapeutics. Nevertheless, many peptide cyclization strategies are not compatible with in vitro display technologies like mRNA display. Here we describe the novel amino acidp‐chloropropynyl phenylalanine (pCPF). pCPF is a substrate for a mutant phenylalanyl‐tRNA synthetase and its introduction into peptides via in vitro translation leads to spontaneous peptide macrocyclization in the presence of peptides containing cysteine. Macrocyclization occurs efficiently with a wide variety of ring sizes. Moreover, pCPF can be reacted with thiols after charging onto tRNA, enabling the testing of diverse ncAAs in translation. The versatility of pCPF should facilitate downstream studies of translation and enable the creation of novel macrocyclic peptide libraries. 

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3. SPIND : a reference-based auto-indexing algorithm for sparse serial crystallography data

   https://doi.org/10.1107/s2052252518014951  

   Li, Chufeng; Li, Xuanxuan; Kirian, Richard; Spence, John_C H; Liu, Haiguang; Zatsepin, Nadia A (January 2019, IUCrJ)

   SPIND(sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability ofSPINDis demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008),Acta Cryst.E64, o1286], which is challenging for commonly used indexing algorithms.SPIND, integrated withCrystFEL[Whiteet al.(2012),J. Appl. Cryst.45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH₂and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability ofSPINDfor indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets.SPINDis written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND. 

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4. Parallel Minimum Cuts in O ( m log ² n ) Work and Low Depth

   https://doi.org/10.1145/3565557  

   Anderson, Daniel; Blelloch, Guy E (December 2023, ACM Transactions on Parallel Computing)

   We present a randomizedO(mlog²n) work,O(polylogn) depth parallel algorithm for minimum cut. This algorithm matches the work bounds of a recent sequential algorithm by Gawrychowski, Mozes, and Weimann [ICALP’20], and improves on the previously best parallel algorithm by Geissmann and Gianinazzi [SPAA’18], which performsO(mlog⁴n) work inO(polylogn) depth. Our algorithm makes use of three components that might be of independent interest. First, we design a parallel data structure that efficiently supports batched mixed queries and updates on trees. It generalizes and improves the work bounds of a previous data structure of Geissmann and Gianinazzi and is work efficient with respect to the best sequential algorithm. Second, we design a parallel algorithm for approximate minimum cut that improves on previous results by Karger and Motwani. We use this algorithm to give a work-efficient procedure to produce a tree packing, as in Karger’s sequential algorithm for minimum cuts. Last, we design an efficient parallel algorithm for solving the minimum 2-respecting cut problem. 

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5. Localization of Cholecystokinin/Sulfakinin Neuropeptides in Biomphalaria glabrata , an Intermediate Host for Schistosomiasis

   https://doi.org/10.1002/cne.70016  

   Rivera, Alana; Bracho‐Rincón, Dina; Miller, Mark W (January 2025, Journal of Comparative Neurology)

   ABSTRACT Snails belonging to the genusBiomphalariaserve as obligatory intermediate hosts for the trematodeSchistosoma mansoni, the causative agent for the most widespread form of schistosomiasis. The simpler nervous systems of gastropod molluscs, such asBiomphalaria, provide advantageous models for investigating neural responses to infection at the cellular and network levels. The present study examined neuropeptides related to cholecystokinin (CCK), a major multifunctional regulator of central nervous system (CNS) function in mammals. A neural transcriptome generated from the CNS ofBiomphalaria alexandrinaincluded a transcript encoding two CCK‐related peptides, designatedBalex‐CCK1 (pEGEWSYDY_(SO3H)GLGGGRF‐NH₂) andBalex‐CCK2 (NYGDY_(SO3H)GIGGGRF‐NH₂). Peptide expression was examined inBiomphalaria glabrataat the mRNA level using the hybridization chain reaction (HCR) protocol and at the protein level using an antibody againstBalex‐CCK1. Expression was detected in 60–70 neurons distributed throughout the CNS, as well as in profuse fiber systems connecting the ganglia and projecting to the periphery. CCK‐like immunoreactive (CCK_li) fibers were also observed on organs associated with the cardiorespiratory (nephridium, mantle, gill) and male reproductive systems. A comparison of mRNA and peptide localization suggested that CCK expression could be regulated at the level of translation. A potential role of these peptides in mediating responses to infection by larval schistosomes is discussed. 

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